Ligand polar atom

Twenty two amino acids come within 5.1 A of the bound retinol molecule. Five of them are within 3.6 A—Lys-40, Thr-53, Arg-58, Trp-104, and Gin-106. In fact, the polar side chains of these residues are close to the bound retinol and again it seems that at least part of the lipid-protein interactions occur through polar atoms. Of particular interest are Lys-40 and Gln-106. As in CRBP, Lys-40 is located above the isoprene tail of the retinol and could interact with the ir-electron field of the ligand. Gln-106, on the other hand, makes a hydrogen bond with the only polar group, the hydroxyl group of the retinol molecule. 

FIGURE 17.1 Non-covalent association between a ligand with two polar atoms (A and B) linked by three methylene units with a receptor containing complementary polarizable atoms (X and Y). Source Adapted from Ref. [9]. 

This ligand polarization favors electrophilic attack on the terminal nitrogen atom. Reactions that activate dinitrogen are of interest as the basis for the fixation of nitrogen as ammonia. 

Discussions of substituent effects on molecular properties considered so far have been performed on a quantitative level. In case of molar rotations of allenes, at least allenes with cr-inductive groups, a quantitative interpretation of the substituent constant X(R) is possible. This interpretation is based upon a quantum-theoretical treatment of the molar rotation of (5 )-(+)-l,3-di-methylallene (3a) (164). According to the theory the parameter X(Me) is related to the group anisotropic polarizability Acr(Me) and a factor /c(Me) which reflects the polarity of the C and the ligand carbon atom. 

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